Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture events.Adaptation to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed genomes.Results Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White Cornish.Signals of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation analysis.Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds.In these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies.Amongst them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold adaptation.Epigenetic factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds.These include genes representing the sine qua non for adaptation to harsh environments.Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.

Analysis of genetic diversity and population structure of Chinese yak breeds (Bos grunniens) using microsatellite markers

Nine Chinese yak breeds （Maiwa, Tianzhu White, Qinghai Plateau, Sibu, Zhongdian, Pali, Tibetan High Mountain, Jiulong, and Xinjiang） and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations, genetic relationship between populations, and population structure for each breed. A total of 206 microsatellite alleles were observed. Mean F-statistics （0.056） for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds. The Neighbor-Joining phylogenetic tree was constructed based on Nei＇s standard genetic distances and two clusters were obtained. The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together. The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one cluster includes yaks from Tibet Autonomous Region and Qinghai Province, one cluster combines Zhongdian, Maiwa, and Tianzhu White, and Jiulong and Xinjiang come into the third cluster. Pali was mainly in the first cluster （90%）, Jiulong was mainly in the second cluster （87.1%）, Zhongdian was primarily in the third cluster （83%）, and the other yak breeds were distributed in two to three clusters. The Gayal was positively left in the fourth cluster （99.3%）.

Metabolomics characterization of colostrum in three sow breeds and its influences on piglets' survival and litter growth rates

Background: Colostrum is the first secretion produced by mammary glands during the hours immediately preceding and succeeding parturition. This secretion differs from milk and represents an essential vehicle of passive immunity,prebiotic compounds and growth factors involved in intestinal development. Most of the literature concerning colostrum composition refers mainly to human and cow; and little is known about pig colostrum metabolome and how it varies between pig breeds and different farrowing parity. Thus, the aim of the present research is to provide new information about pig colostrum composition and the associations between metabolites, the sows' breed and the survival and growth rates of their litters.Results: Colostrum samples were gathered from 58 parturitions of sows belonging to three different breeds chosen for their importance in Italian heavy pig production: 31 Large White, 15 Landrace and 12 Duroc respectively. The defatted and ultrafiltered colostrum samples were analysed using1 H–NMR spectroscopy. Principal Components Analysis(PCA) was assessed on the obtained spectra. In addition, using a Stepwise Regression and a Linear Regression analyses the metabolites named after the signals assignment were tested for their associations with piglets' performances.Twenty-five metabolites were identified, comprehending monosaccharides, disaccharides(such as lactose), organic acids(lactate, citrate, acetate and formate), nitrogenous organic acids(such as creatine) and other compounds,including nucleotides. PCA results evidence a clustering due to breed and season effects. Lactose was the main compound determining the assignment of the samples into different clusters according to the sow breed. Furthermore, some metabolites showed to be associated with piglets' performance and survival traits: acetate and taurine were positively related to litter weight gain and piglets' survival rate, respectively, while dimethylamine and cis-aconitate were linked to new-borns' impaired ability to survive.Conclusions: The results obtained suggest that colostrum composition is affected by breed, which, together with environmental conditions, may cause changes in colostrum metabolites content with possible consequences on piglets' performances. Among the identified metabolites, acetate, taurine, dimethylamine and cis-aconitate showed consistent associations with piglets' survival rate and litter weight gain, implying that these compounds may affect new-borns' ability to survive.

Variations in porcine colostrum oligosaccharide composition between breeds and in association with sow maternal performance

Background:Oligosaccharides(OS)are indigestible carbohydrates naturally found in milk.The composition of porcine colostrum OS may influence the growth and the health of the neonate and consuming optimal concentrations of OS may reduce piglet susceptibility to illness.In this manner,targeted supplementation of animal feed with OS is being explored as a health management tool in the livestock industry.The variation in OS composition between different breeds of pig and its association with the litter performance is currently unknown.The aim of this study was to characterize the colostrum OS composition from sows of different breed and parity and correlate this data with sow maternal traits.Methods:Eighty-three colostrum samples from parities 1 to 8 were gathered from 3 different breeds of sow:44 Large White sows,27 Landrace sows and 12 Duroc sows.Samples were taken between the birth of the first and the last piglet from sows that were not pharmacologically induced to farrow.OS were purified from the samples and analysed by MALDI-ToF mass spectrometry(21 OS compositions detected).The farrowing season and the maternal data were recorded for each sow,including the number of live piglets and the litter body weight at birth,at day(d)3 and at weaning.Results:Five OS compositions,including isomers of the bifidogenic Sialyllactose,Lacto-N-Tetraose and Lacto-NHexaose series,were detected in all the samples.Twelve other OS were identified in at least 50%of samples,and their abundances were affected by breed(P<0.05;6 of 12),marginally affected by season(P<0.10;3 of 12)and never by parity number.The abundances of each OS component were standardized by Z-score scaling(μ=0 and SD=1),transformed by principal component analysis,and four similarity clusters were generated.Cluster membership was associated with litter weight gain within 3 days(P=0.063)and at weaning(P<0.05),but not with piglet mortality within 3 days.Conclusions:OS composition of colostrum may partially explain the variability in maternal performance within and between different breeds of sow.The obtained OS data can provide useful information for the development of novel prebiotic food supplements for suckling and weaning pigs.

Pattern of Development in Foals from Four Different Breeds between Birth and Weaning

Several studies have shown a major development in height and cannon bone circumference in foals from birth to weaning and from different breeds. However, in Brazil, there is little information about foal development. For this reason, this study has used data on foals from seven different farms in Pernambuco, Northeast Brazil, where horses have a major economic importance. The aim of this study was to compare foal’s development from four breeds and to develop a regression formula in order to estimate such development. It was used data from 210 suckling foals (Arabians n = 18, Campolina n = 86, Mangalarga Marchador n = 42 and Quarter Horses n = 64), raised in similar management practices. Their height at withers, heart girth, and cannon bone girth were measured monthly from birth to weaning. Data we reanalyzed by ANOVA and Tukey Test, with P established in 5%. The highest mean of height at withers was observed in the Arabian foals, and it was similar to Campolina and Mangalarga Marchador foals. The last breed presented a higher percentage of gain in height (~36%) and higher heart girth. On the other hand, Campolina foals had the highest mean of cannon bone girth. There was a significant interaction between breed and development phase in heart and cannon bone girths. All regression for mulas obtained from this data was very significant, and it was showed that they can predict height at withers in the four breeds studied. Heart and cannon bone girths showed medium value of R2 and large significance. It is important to highlight that fetal programing produces significant impact on foal development, even after weaning. So, this study would have observed some more changes if its scope had been extended beyond this phase.

Comparison of Analyses of Genetic Structure among Chinese Indigenous Chicken Breeds using Distance-based and Model-based Methods

The Nei's improved genetic distance(DA)and gene flow(Nm)were measured using sixteen microsatellite markers.Dendograms based on DA genetic distance using the neighbor-joining(NJ)method and STRUCTURE program were constructed to analyze the genetic structure and relationship among 10 Chinese indigenous chicken breeds.The results showed that dendograms of DA genetic distance using the NJ method divided the 10 chicken breeds into two main clusters;one consisted of breeds of low weight body(CHA,TTB,XIA,GUS and BAI),the other contained heavier breeds(LAN,DAG,YOU,XIS and LUY).In the lighter breeds,TIB and CHA clustered together,as did XIA and GUS.In the heavier breeds,XIS and LUY was clustered together in one branch,but LAN,DAG and YOU clustered in independent branches.The results were consistent with Nm estimates among the 10 indigenous chicken breeds.The STRUCTURE program properly inferred the presence of genetic structure despite not pre-defining the origin of individuals.The genetic cluster inferred by STRUCTURE was basically the same as that from the DA distance clustering method.An advantage of the STRUCTURE program was its ability to identify the migrants and admixed individuals in the 10 chicken populations;this could not be achieved by use of the DA distance clustering method.

The SNPs Analysis of the Exons of Three Genes of MyoD Gene Family in Seven Swine Breeds (Line)

The study objects includes seven swine breeds： Minzhu, Sanjiangbaizhu, Yorkshire, Landrace, Junmuyihao, Duroc and Double muscle Yorkshire. According to the sequences of MyoG, MyoD and Myf5 of swine in GenBank, seventeen pairs of primers for MyoG, MyoD and Myf5 were designed. PCR-SSCP technology was applied to detect SNPs of the exons of the three genes. The results showed that no polymorphism was in MyoG and MyoD, and some SNPs were in three exons of Myf5. There was one mutant site in the first exon of Myf5 （G → C）, three mutant sites in the second exon of Myf5 （C → A, A → G and G → A）; in the third exon of Myf5, there was one base A deficiency at 3 387 bp, three bases T deficiency at 3417 bp, one mutant site at 3443 bp （T → C）. This study obtained a tendency conclusion that gene frequency of allele M of Myf5 on the one hand is positively correlated with lean meat percentage, on the other hand is correlated with the orientation of selective breeding; it also deduced that allele F is possibly correlated with high lean meat percentage. Through statistical analysis, allele A, B, C of Myf5 have no obvious correlation with lean meat percentage of different swine breeds. In addition, the high polymorphism of Myf5 showed that seven swine breeds are rich in genetic variation, and have high selective competency.

An Empirical Analysis of Farmers' Rabbit Breeds Purchase and Its Influencing Factors

In this paper,based on the survey data on farmers in 14 provinces and cities nationwide provided by China Rabbit Research System,we analyze the farmers' rabbit breeds selection,purchase channels and the demand for new varieties of rabbits as well as the problems in the course of rabbit usage. We make an empirical analysis of the factors influencing farmers' rabbit demand,and put forth the recommendations for farmers' rabbit breeds usage and to improve the promotion of new varieties of rabbits.

Small Optical Product Breeds Large Industry

China is the world’s largest consumer market for eyeglasses,with the total market volume reaching 80billion yuan.Accordingly,the market has a group of 800 million consumers demanding eyeglasses.The consumers are from different ages。

Impact of environmental and social factors on genotypic and phenotypic diversity of some local Sudanese sheep breeds

This mini review aimed to discuss and compare the findings of a genotypic study done by Gor-nas et al., 2011 and some environmental and social factors discussed previously in Sudan. The main conclusion was the agreement of the genotypic analysis with the previous observations done on the phenotypic part. The important recommendation was to support the nomadic system so as to preserve the biodiversity of livestock in Sudan.

Preliminary Comparative Physiological and Biochemical Study of Five Different Goat Breeds Inhabiting Saudi Arabia

Three arbitrary chosen enzymes were examined by native-polyacrylamide gel electrophoresis to investigate physiological and genetic variations among five different goat breeds inhabiting Saudi Arabia. The goat breeds were Pakistani, Tihami, Syrian, Masri and Aardi while the investigated enzymes were alkaline phosphatase (ALP), malate dehydrogenase (Mdh) and malic enzyme (ME). Six polymorphic loci with six monomeric alleles have been recorded in all studied breeds. The second locus of ME was characteristic of Syrian breed where it showed dimeric alleles. The similarity matrix that has been calculated according to the number of sharing bands indicated that these breeds have been divided into two groups: Pakistani and Tihami as one group while the other three breeds clustered in another group. The activity of the metabolic enzymes (Mdh and ME) showed concordance with the constructed relationship where the percentage amounts of these enzymes showed significant variations between the two groups more than that occurred within each group. Mdh was expressed in the second group more than in the first while ME showed, nearly, equal expression in the different breeds. Both genetic and physiological results agreed in clustering the studied breeds into Pakistani and Tihami in one group and the other three breeds in another group. This division was based on a few gene loci and a few sampling size and it needs to be supported by collecting more genetic data and more sampling size in a further molecular study.

Study on the Effect of ESR and FSH β Genes on Litter Size in Local Northeast Three Pig Breeds

The method of PCR RFLP was used to analyze the effects of ESR and FSH β genotypes on the litter size,especially the corresponding changes with the difference of genotype distributions in the Min,Sanjiang and Junmu I pigs.The results show that the ESR and FSH β genes are the major genes of litter size;the heterozygous genotype for ESR as well as for FSH β locus has a more litter size than others.However,the combined genotype ABDD means a more litter size than other genotypes,the frequencies of the heterozygous genotypes in Sanjiang and Junmu I are lower than in Min which maybe one of the most important reasons for the little litter sizes of those two breeds.

A Comparative Study of the Karyotypes from Four Egg-type Fowl Breeds

By adopting the method based on colchicine-hypotonic-air drying technique with bone marrow cells, the paper presents the chromosome of four egg-type fowl breeds. The diploid chromosome 2n=78, chromosomal morphology are very similar and sex chromosome type are ZZ (♂) and ZW(♀) in four egg-type fowl breeds. According to standard of Leven in 1964, the euchromosome and sex chromosome of four breeds are measured and compared in relative length arm ratio and centromere index of each chromosome including all the microchromosome. The morphology of these chromosome is described as follows: pair1, 2, 8 and ZW are metacentric, pair 4 and 6 are submetacentric, and the rest is telocentric.

Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

Background:A large number of pig breeds are distributed around the world,their features and characteristics vary among breeds,and they are valuable resources.Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.Results:In this study,we performed GWAS using a standard mixed linear model with three types of genome variants(SNP,InDel,and CNV)that were identified from public,whole-genome,sequencing data sets.We used 469 pigs of 57 breeds,and we identified and analyzed approximately 19 million SNPs,1.8 million InDels,and 18,016 CNVs.We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes,which included coat color,ear shape,gradient zone,body weight,body length,and body height.A total of 37 candidate genes was identified,which included 27 that were reported previously(e.g.,PLAG1 for body weight),but the other 10 were newly detected candidate genes(e.g.,ADAMTS9 for coat color).Conclusion:Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.

Effect of Age and Breeds of Cattle on Carcass and Meat Characteristics of Arsi, Boran, and Harar Cattle in Ethiopia

The objective of this study was to determine the effect of age and breed of cattle on carcass and meat characteristics in Ethiopia. A total of 39 (Arsi 11, Boran 14 and Harar 14) cattle breeds with age categories of <3, 4 - 6, and 7 - 9 years were used for the study. The bulls were purchased from their respective production system of mixed crop livestock system (Arsi and Harar) and Ranch (Boran). Parameters such as live and carcass weight, meat yield percent, fat characteristics, and primal beef cuts were evaluated. Complete randomized design was used for the study. The live weight of bulls at <3, 4 - 6 and 7 - 9 years ranged 135 - 183, 167 - 181, and 155 - 433 kg, respectively. The carcass weight, dressing percentage, meat yield percent, forequarter, hindquarter, rib eye area, and fat thickness ranged 57 - 209.73 kg, 41.8% - 51.6%, 32% - 58%, 11.7 - 56.42 kg, 14.04 - 45.34 kg, 4.78 - 10.25 square inches and 0.18 - 0.38 inches, respectively. At an early age category (<3 years) meat yield percentage of Arsi, Boran and Harar breeds were 50.86, 30 and 18.72, respectively, and as age category shifted from one age category to the next Harar increased by 13× and Boran by 2.9× and Arsi decreased by -0.93×. The mean rib percentage of Arsi, Boran and Harar were in the range of 7.98 - 9.57, 8.62 - 10.44 and 7.08 - 8.83, respectively. Breed and age of bulls had significantly affected primal meat cuts. Meat yield was predicted from live and hot carcass weight with coefficient determination (R2) of 70.66% and 74.75%, respectively. From the study, it was concluded that age and breeds of cattle had significantly influence on carcass and meat characteristics. Therefore, to determine whether variations were due to genetic or environmental cause’s evaluation of the three breeds under similar feeding condition was recommended.

Effect of buffalo bull breeds on developmental competence and vitrification ofin-vitro produced embryos

Objective:To assess effect of buffalo bull breed on the development and cryotolerence of the in vitro produced embryos.Methods: Three types of frozen semen were adopted;Egyptian, Italian and cross-bred (Egyptian-Italian) breeds were used for in-vitro fertilization and vitrification of their embryos. Oocytes were collected from buffalo ovaries and maturedin vitrofor 24 h, then they were fertilized using the three semen breeds. The produced embryos of morula and blastocysts were vitrified using ethylene glycol and dimethyl sulfoxide then evaluated for their viability after warming.Results: The cleavage and blastocysts rates significantly declined in oocytes fertilized by Egyptian (P<0.01) than in Italian (P<0.05) and crossbred (P<0.05) frozen semen. After embryo vitrification, there were no significant differences among the three breeds in the percentages of morphologically viable embryos evaluated directly after warming and at 24 h post-culture. Conclusions:Thein vitro fertilization response to frozen-thawed semen varies between breeds;however, the resistance of produced embryos to the damage effect of vitrification does not vary.

Polymorphism Analysis on Partial Sequence of Pig Obese Gene of Different Breeds by PCR- SSCP

Polymorphisms of porcine ob exon 1 and exon 2 among different breeds including Landrace, Duroc, Min pig, Yorkshire pig, double-muscled Yorkshire, Sanjiang pig, wild boar and cross bred pig were analyzed by PCR-SSCP in the current study. Three pairs of primers according to the ob cDNA sequence obtained from GenBank database were designed to amplify the first two exons, which were then genotyped by SSCP. The T to C transversion was found in exon 2, which resulted in 3 genotypes named AA, AB and BB, respectively in these different porcine breeds. There was only genotype of BB in the Min pig, while no allele B was detected in double-muscled Yorkshire, and the 3 genotypes all existed in other breeds. There was significant difference on the genotype frequencies in various breeds. There was a trend that the frequency of allele A was positively associated with muscle ratio distribution on the one hand, and on the other hand, it was linked to the selected direction. So the allele A could be used as a selective marker of high muscle ratio in pig breeding.

Cultivation of New Breeds of Guizhou Heima Goat

To culture new breeds of Guizhou Heima goat, establishing open nucleus br^ding system in farm was adopted to develop comprehensive selection index and establish BLUP model to estimate breeding value, so as to guide assortative mating and selection improvement. The results showed that the body weights of yearling ram and ewe in nucleus herd were （29.77± 5.51 ） kg and （25.18 ± 5.67 ） kg, while those of adult ram and adult ewe were （40.08 ± 7.73 ） kg and （ 34.90 ±6.56） kg, respectively; the body weights of yearling ram and ewe in basic herd were （26.59 ±3.68） kg and （24.139 ±4.60） kg, while those of adult ram and adult ewe were （35.33 ± 4.09） kg and （32.16 ± 6.83 ） kg, respectively; the lambing rate was 152.33 % ; the slaughter rate was 48.50%, and the net meat rate was 38.94%. New breeds of Guizhou Heima goat had significantly improved production performance and breed uniformity, with stable genetic performance.

Characterization, conservation and sustainability of endangered animal breeds in Campania (Southern Italy)

Conservation of such animal genetic resources and sustainable development of their products seems to be one of the most important steps to be taken to save endangered animal breeds from the widespread use of cosmopolitan and more productive breeds. Indeed, the protection and conservation of biodiversity of animal breeds adapted to particular environmental conditions is essential to prevent irreversible erosion of genes and gene combinations. A special project to characterize and conserve eight endangered breeds of various animal species raised in Campania (southern-Italy) is reported in this paper along detailed descriptions of all breeds. Some strategies for their characterization and conservation are reported and discussed.

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozy-gosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indige-nous chickens possessed more genetic diversity than that reported in many other countries. The fixa-tion coefficients of subpopulations within the total population (FST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within con-servation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken re-sources.